remake.yml

sources:
  - createlookup.R

packages:
  - taxize
  - R6
  - yaml
  - digest
  - devtools
  - downloader

targets:
  all:
    depends:
      - plant_lookup.csv
      - R/sysdata.rda

  VascularPlantFamilies:
     command: getTplVascularPlantFamilies()

  downloadTPL:
    command: downloadPlantList(VascularPlantFamilies)

  tplGenera:
    command: combineGeneraLists(downloadTPL,VascularPlantFamilies)

  additions:
    command: read_csv(file="source_data/Additions.csv",row.names=1)

  tplGenera_patched:
    command: patchTPL(tplGenera,additions)

  lookupRaw:
    command: matchPlantListFamiliesToApweb(tplGenera_patched)

  lookupPatch:
    command: read_csv("source_data/genus_order_lookup_fae.csv")

  badTPL:
    command: read_csv("source_data/badGeneraFamilyPairs.csv")

  lookupFixed:
    command: fixFernsAndOtherProblems(lookupRaw, lookupPatch, badTPL)

  plant_lookup.csv:
    command: outputFlatFile(lookupFixed, target_name)

  source_data/Spermatophyta_Genera.csv:
    download: http://datadryad.org/bitstream/handle/10255/dryad.59001/Spermatophyta_Genera.csv?sequence=2

  higherOrderTaxonomy:
    command: readHigherOrderTaxonomy("source_data/Spermatophyta_Genera.csv", lookupFixed)

  R/sysdata.rda:
    command: packageData(higherOrderTaxonomy, target_name)